Generates TSV reports from Philosopher workspace binaries.
This module runs Philosopher report to generate TSV result files (psm.tsv, peptide.tsv, protein.tsv, ion.tsv) from .meta/ workspace binaries.
It is used after PHILOSOPHERFILTER (with skip_report=true) followed by FreeQuant or LabelQuant, which update the .meta/ binaries with quantification data.
The module re-initializes the workspace and re-annotates the database to ensure accessibility, since the workspace may come from a different task's work directory.
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Sample/experiment metadata |
| results_dir | path | Directory containing .meta/ workspace binaries from PHILOSOPHERFILTER/FREEQUANT/LABELQUANT |
| report_cli | val(string) | Report CLI flags (e.g., --msstats) |
| fasta | path | Philosopher database with decoys/contaminants from PHILOSOPHERDATABASE |
| decoy_tag | val(string) | Decoy protein prefix from the workflow database.decoy-tag (via getDecoyTag()) |
| Channel | Type | Description |
|---|---|---|
| results_dir | tuple(val, path) | Output directory ${prefix} containing all TSV files |
| psms | tuple(val, path) | ${prefix}/psm.tsv PSM-level results with quantification intensities |
| peptides | tuple(val, path) | ${prefix}/peptide.tsv peptide-level results |
| proteins | tuple(val, path) | ${prefix}/protein.tsv protein-level results |
| ions | tuple(val, path) | ${prefix}/ion.tsv ion-level results (optional) |
| versions_philosopher | topic: versions | Philosopher version |
| versions_fragpipe | topic: versions | FragPipe version |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional command-line arguments for philosopher report |
| ext.prefix | ${meta.id} |
Output directory name |
| ext.fragpipe_tools_dir | /fragpipe_bin/fragpipe-24.0/fragpipe-24.0/tools |
FragPipe tools directory |
The licensed FragPipe image given with --fragpipe_container.
Used in the FRAGPIPE_QUANT subworkflow (subworkflows/local/fragpipe_quant/main.nf) after PHILOSOPHERLABELQUANT to generate final TSV files with correct TMT reporter ion intensities.